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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BSRD Resource Report Resource Website 10+ mentions |
BSRD (RRID:SCR_004249) | BSRD | data or information resource, data repository, database, service resource, storage service resource | A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets. | srna target, srna, small regulatory non-coding rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23203879 | Acknowledgement requested, The community can contribute to this resource | biotools:bsrd, OMICS_01533 | https://bio.tools/bsrd | SCR_004249 | BSRD - Bacterial Small Regulatory RNA Database, Bacterial Small Regulatory RNA Database | 2026-09-19 12:50:35 | 29 | |||||
|
CDP Resource Report Resource Website 10+ mentions |
CDP (RRID:SCR_004236) | CDP | data or information resource, funding resource, portal, topical portal | National program to improve the diagnosis and assessment of cancer by moving scientific knowledge into clinical practice by coordinating and funding resources and research for the development of innovative in vitro diagnostics, novel diagnostic technologies and appropriate human specimens. The Cancer Diagnosis Program is divided into four branches: Biorepository and Biospecimen Research Branch (BBRB), Diagnostic Biomarkers and Technology Branch (DBTB), Diagnostics Evaluation Branch (DEB), and the Pathology Investigation and Resources Branch (PIRB). | cancer research, cancer funding, cancer research funding |
is listed by: OMICtools has parent organization: DCTD |
Cancer | NCI | Available to cancer researchers | OMICS_01536 | SCR_004236 | Cancer Diagnosis Program | 2026-09-19 12:50:35 | 19 | |||||
|
DRUT Resource Report Resource Website |
DRUT (RRID:SCR_004351) | DRUT | software resource | Software for Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data. | c++, reconstruction, frequency estimation, transcript, rna-seq, annotation |
is listed by: OMICtools has parent organization: Georgia State University; Georgia; USA |
NSF IIS-0546457; NSF IIS-0916401; NSF IIS-0916948 |
PMID:23202426 | OMICS_01273 | SCR_004351 | Discovery and Reconstruction of Unannotated Transcripts | 2026-09-19 12:50:36 | 0 | ||||||
|
PSGInfer Resource Report Resource Website |
PSGInfer (RRID:SCR_000243) | PSGInfer | software resource | Software for inference of alternative splicing from RNA-Seq data with probabilistic splice graphs. | alternative splicing, rna-seq, probabilistic splice graph |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:23846746 | Free, Available for download, Freely available | OMICS_01967 | SCR_000243 | PSGInfer: Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs | 2026-09-19 12:49:18 | 0 | ||||||
|
Cascleave Resource Report Resource Website |
Cascleave (RRID:SCR_000197) | Cascleave | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A novel tool developed using Java program for the high-throughput in silico identification of substrate cleavage sites for various caspases from the amino acid sequences of the substrates. | matlab |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:24149049 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01670 | SCR_000197 | Cascleave 2.0 - Caspase substrate cleavage site prediction, Cascleave 2.0 | 2026-09-19 12:49:17 | 0 | ||||||
|
HEM Resource Report Resource Website |
HEM (RRID:SCR_000194) | HEM | software resource | Software package that fits heterogeneous error models for analysis of microarray data | differential expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Virginia; Virginia; USA |
PMID:15044230 | Free, Available for download, Freely available | OMICS_01970 | SCR_000194 | HEM - Heterogeneous error model for identification of differentially expressed genes under multiple conditions | 2026-09-19 12:49:17 | 0 | ||||||
|
Molegro Virtual Docker Resource Report Resource Website 1+ mentions |
Molegro Virtual Docker (RRID:SCR_000190) | Molegro Virtual Docker | software resource | An integrated platform for predicting protein-ligand interactions, the visualization of new ideas and analyzing protein targets. | protein ligand, protein target, visualization, integrated platform | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01603 | SCR_000190 | 2026-09-19 12:49:17 | 9 | ||||||||
|
MRNet Resource Report Resource Website 1+ mentions |
MRNet (RRID:SCR_000225) | MRNet | software resource | A software-based network that provides efficient multicast and reduction communications for parallel and distributed tools and systems. Some key features of this resource include scalable data aggregation, multiple concurrent data channels and high-bandwidth communication. | is listed by: OMICtools | DOI:10.1145/1048935.1050172 | Free, Available for download, Freely available | OMICS_01686 | SCR_000225 | MRNet: A Multicast/Reduction Network | 2026-09-19 12:49:18 | 1 | |||||||
|
RSEM Resource Report Resource Website 100+ mentions |
RSEM (RRID:SCR_000262) | data analysis software, data processing software, software application, software resource | Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. | quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:21816040 | Free, Available for download, Freely available | OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 | https://github.com/deweylab/RSEM, https://github.com/deweylab/RSEM/releases, https://bio.tools/rsem, https://sources.debian.org/src/rsem/ | SCR_000262 | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-09-19 12:49:19 | 115 | ||||||
|
MS-Spectre Resource Report Resource Website 1+ mentions |
MS-Spectre (RRID:SCR_000266) | software resource | Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02496 | SCR_000266 | Mass Spectrometry Analysis Software | 2026-09-19 12:49:19 | 2 | ||||||||
|
M(at)CBETH Resource Report Resource Website |
M(at)CBETH (RRID:SCR_000265) | M(at)CBETH | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. Web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset. | microarray, classification, performing microarray classification, |
is listed by: OMICtools has parent organization: Catholic University of Leuven; Flemish Brabant; Belgium |
PMID:15890742 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02292 | SCR_000265 | MicroArray Classification BEnchmarking Tool on Host server | 2026-09-19 12:49:19 | 0 | ||||||
|
BLASTPLOT Resource Report Resource Website |
BLASTPLOT (RRID:SCR_000162) | BLASTPLOT | software resource | A PERL module that can quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. This software generates PNG graphs for all of the reference sequences associated with a BLAST result set. | perl, blast, short sequence, primer, png, png graph |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24685334 | Free, Available for download, Freely available | OMICS_01433 | SCR_000162 | 2026-09-19 12:49:17 | 0 | |||||||
|
GemSIM Resource Report Resource Website |
GemSIM (RRID:SCR_000167) | GemSIM | software resource | A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface. | bioinformatics, simulation, sequencing, dna, rna, empirical models, Python, command-line, user interface, metagenomic, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge is required by: Wessim |
PMID:22336055 DOI:10.1186/1471-2164-13-74 |
Free, Available for download, Freely available | OMICS_01507, biotools:GemSIM | https://bio.tools/GemSIM | SCR_000167 | 2026-09-19 12:49:17 | 0 | ||||||
|
GMATo Resource Report Resource Website 1+ mentions |
GMATo (RRID:SCR_000165) | data analysis software, data processing software, sequence analysis software, software application, software resource | A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable. | simple sequence repeat, ssr, microsatellite, genomic, marker design, sequence analysis software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23861572 | Free, Available for download, Freely available | OMICS_00106 | SCR_000165 | Genome-wide Microsatellite Analyzing Tool, Genome Microsatellite Analyzing Tool, Genome-wide Microsatellite Analyzing Tool (GMATo) | 2026-09-19 12:49:17 | 1 | |||||||
|
ProteinProphet Resource Report Resource Website 10+ mentions |
ProteinProphet (RRID:SCR_000286) | software resource | Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:14632076 | OMICS_02521, biotools:proteinprophet | https://bio.tools/proteinprophet | SCR_000286 | 2026-09-19 12:49:20 | 11 | ||||||||
|
iFad Resource Report Resource Website |
iFad (RRID:SCR_000271) | iFad | software resource | An R software package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines. | r, gene expression, drug sensitivity, analysis, drug-pathway association, gene-pathway, pathway, gene, drug |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
PMID:22581178 | Free, Available for download, Freely available | OMICS_01959 | SCR_000271 | 2026-09-19 12:49:19 | 0 | |||||||
|
GramCluster Resource Report Resource Website |
GramCluster (RRID:SCR_000272) | GramCluster | software resource | Software implementing a fast and accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets. | 16s sequence, cluster |
is listed by: OMICtools has parent organization: University of Nebraska; Nebraska; USA |
PMID:21167044 | Free, Available for download, Freely available | OMICS_01956 | SCR_000272 | 2026-09-19 12:49:19 | 0 | |||||||
|
Postgwas Resource Report Resource Website |
Postgwas (RRID:SCR_000156) | software resource | A comprehensive software toolkit for post-processing, visualization and advanced analysis of GWAS results. | standalone software, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:23977141 | Free, Available for download, Freely available | OMICS_04393 | SCR_000156 | 2026-09-19 12:49:17 | 0 | ||||||||
|
DESeq Resource Report Resource Website 500+ mentions |
DESeq (RRID:SCR_000154) | DESeq | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression. | gene expression, binomial, differential, negative binomial distribution, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
PMID:20979621 DOI:10.1186/s13059-014-0550-8 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01306, biotools:deseq | https://bio.tools/deseq, https://sources.debian.org/src/r-bioc-deseq2/ | SCR_000154 | 2026-09-19 12:49:17 | 529 | ||||||
|
RNASeqReadSimulator Resource Report Resource Website 1+ mentions |
RNASeqReadSimulator (RRID:SCR_000270) | RNASeqReadSimulator | software resource | A software tool to generate simulated single-end or paired-end RNA-Seq reads. # It allows users to randomly assign expression levels of transcripts and generate simulated single-end or paired-end RNA-Seq reads. # It is able to generate RNA-Seq reads that have a specified positional bias profile. # It is able to simulate random read errors from sequencing platforms. # The simulator consists of a few simple Python scripts. All scripts are command line driven, allowing users to invoke and design more functions. | rna-seq, command line | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01964 | SCR_000270 | 2026-09-19 12:49:19 | 1 |
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